Merge branch 'master' into enh/JSONFileInterface

Conflicts:
	CHANGES

Author: oesteban

.gitignore

@@ -13,3 +13,4 @@
 .settings
 .pydevproject
 .idea/
+/documentation.zip

CHANGES

@@ -2,6 +2,15 @@ Next release
 ============
 
 * ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
+* ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
+* BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
+* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
+* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
+* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
+       New options also include choice of tracker, interpolator, stepsize and 
+       curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
+* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
+* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
 * ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
 * ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 
 	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
@@ -14,6 +23,8 @@ Next release
 	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
 * FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
 * FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
+* ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
+* ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
 
 Release 0.10.0 (October 10, 2014)
 ============

doc/users/config_file.rst

@@ -120,6 +120,11 @@ Execution
     characters will be replaced by their hash. (possible values: ``true`` and
 	``false``; default value: ``true``)
 
+*poll_sleep_duration*
+    This controls how long the job submission loop will sleep between submitting
+    all pending jobs and checking for job completion. To be nice to cluster
+    schedulers the default is set to 60 seconds.
+
 Example
 ~~~~~~~
 

doc/users/plugins.rst

@@ -140,7 +140,7 @@ particular node might use more resources than other nodes in a workflow.
 LSF
 ---
 
-Submitting via LSF is almost identical to SGE above:
+Submitting via LSF is almost identical to SGE above above except for the optional arguments field:
 
        workflow.run(plugin='LSF')
 
@@ -149,6 +149,18 @@ Optional arguments::
   template: custom template file to use
   bsub_args: any other command line args to be passed to bsub.
 
+SLURM
+-----
+
+Submitting via SLURM is almost identical to SGE above except for the optional arguments field:
+
+       workflow.run(plugin='SLURM')
+
+Optional arguments::
+
+  template: custom template file to use
+  sbatch_args: any other command line args to be passed to bsub.
+
 HTCondor
 --------